Re: [Freesurfer] Contrasts in GLM

Linda Zhang wrote:

Hi Doug,

Thanks for the clarification. If I were to add another two class variables (patient and subject, for example) and I wanted to see if they affected thickness, assuming they come after gender in the fsgd file, would the contrasts then be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]?

Sorry, I can't remember what your design is (I answer a lot of emails and they often blend together). Can you refresh my memory?

From the powerpoint slides, there's an example where two contrast matrices are used (age, gender), what kind of output would that produce?

It would produce results (p-values, eg) for each of the contrasts. This allows you to run one command instead of one for each contrast.

/home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh doesn't exist, I'm not sure why...

Your mris_preproc failed or you are not in the directory that has this file. doug

Cheers, Linda

On 3 December 2011 01:26, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

does
/home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh
exist?
doug

Linda Zhang wrote:

    Dear all,

    I think I figured out the contrasts (I'm using [0 0 0 0 0.5
    0.5 0 0]...is that correct?) but I've come across an error
    when trying to do the next step in the tutorial.

    I didn't cache the data during recon-all, so I ran the following:

    mris_preproc --fsgd MMSE-AD.fsgd --target fsaverage --hemi lh
    --meas thickness --out lh.MMSE-AD.thickness.00.mgh

    It seemed to run smoothly (I've attached the log below) so I
    ran the next step:

    mri_surf2surf --hemi lh --s fsaverage --sval
    lh.MMSE-AD.thickness.00.mgh --fwhm 10 --cortex --tval
    lh.MMSE-AD.thickness.10.mgh

    I got the following error:

    Reading source surface reg
    /home/virtualuser/freesurfer/subjects/fsaverage/surf/lh.sphere.reg
    Loading source data
    mghRead(/home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh,
    -1): could not open file
    ERROR: could not read lh.MMSE-AD.thickness.00.mgh as type 3

    Can anyone tell me where the problem is?  Thanks!

    Cheers,
    Linda

    The log for mris_preproc (truncated to the last subject and
    last line):

    ---------------------------------------------------
    #@# 12/12 avo1249 Fri Dec  2 18:20:04 HKT 2011 --------------
    -----------------------
    mri_surf2surf --srcsubject avo1249 --srchemi lh --srcsurfreg
    sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg
    sphere.reg --tval ./tmp.mris_preproc.18275/avo1249.12.mgh
    --sval
    /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness
    --sfmt curv --noreshape --no-cortex
    Source registration surface changed to sphere.reg
    Target registration surface changed to sphere.reg
    srcsubject = avo1249
    srcval     =
    /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness
    srctype    = curv
    trgsubject = fsaverage
    trgval     = ./tmp.mris_preproc.18275/avo1249.12.mgh
    trgtype    =
    srcsurfreg = sphere.reg
    trgsurfreg = sphere.reg
    srchemi    = lh
    trghemi    = lh
    frame      = 0
    fwhm-in    = 0
    fwhm-out   = 0
    label-src  = (null)
    label-trg  = (null)
    OKToRevFaceOrder  = 1
    Reading source surface reg
    /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.sphere.reg
    Loading source data
    Reading curvature file
    /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness
    Reading target surface reg
    /home/virtualuser/freesurfer/subjects/fsaverage/surf/lh.sphere.reg
    Done
    Mapping Source Volume onto Source Subject Surface
    surf2surf_nnfr: building source hash (res=16).
    Surf2Surf: Forward Loop (163842)

    surf2surf_nnfr: building target hash (res=16).
    Surf2Surf: Reverse Loop (121128)
    Reverse Loop had 15750 hits
    Surf2Surf: Dividing by number of hits (163842)
    INFO: nSrcLost = 0
    nTrg121 = 151248, nTrgMulti = 12594, MnTrgMultiHits = 2.2506
    nSrc121 = 78171, nSrcLost =     0, nSrcMulti = 42957,
    MnSrcMultiHits = 2.36099
    Saving target data
    Saving to ./tmp.mris_preproc.18275/avo1249.12.mgh



    -----------------------
    mri_concat ./tmp.mris_preproc.18275/avo0015.1.mgh
    ./tmp.mris_preproc.18275/avo0260.2.mgh
    ./tmp.mris_preproc.18275/avo0403.3.mgh
    ./tmp.mris_preproc.18275/avo0441.4.mgh
    ./tmp.mris_preproc.18275/avo0493.5.mgh
    ./tmp.mris_preproc.18275/avo0622.6.mgh
    ./tmp.mris_preproc.18275/avo0677.7.mgh
    ./tmp.mris_preproc.18275/avo0920.8.mgh
    ./tmp.mris_preproc.18275/avo1086.9.mgh
    ./tmp.mris_preproc.18275/avo1206.10.mgh
    ./tmp.mris_preproc.18275/avo1241.11.mgh
    ./tmp.mris_preproc.18275/avo1249.12.mgh --o
    lh.MMSE-AD.thickness.00.mgh



    On 2 December 2011 11:42, Linda Zhang <lzhang87@gmail.com
    <mailto:lzhang87@gmail.com> <mailto:lzhang87@gmail.com
    <mailto:lzhang87@gmail.com>>> wrote:

       Dear all,

       I have a bit of an amateur question.  I've read the slides and
       tutorial for group analysis, but I'm still confused about the
       contrasts.  I made my fsgd file, which contains two groups:
    M and
       F.  I also have three continuous variables: Age, MMSE,
    Education.     I would like to test whether thickness is
    correlated with MMSE
       scores, after controlling for gender, age, and education.  What
       should my contrast file be in this case?
       Thanks for the help!

       Cheers,
       Linda


    ------------------------------------------------------------------------

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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 Fax: 617-726-7422

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